Moving beyond metagenomics to find the next pandemic virus

I was asked to write a commentary for the Proceedings of the National Academy of Sciences to accompany an article entitled SARS-like WIV1-CoV poised for human emergence. I’d like to explain why I wrote it and why I spent the last five paragraphs railing against regulating gain-of-function experiments.

Towards the end of 2014 the US government announced a pause of gain-of-function research involving research on influenza virus, SARS virus, and MERS virus that “may be reasonably anticipated to confer attributes to influenza, MERS, or SARS viruses such that the virus would have enhanced pathogenicity and/or transmissibility in mammals via the respiratory route.”

From the start I have opposed the gain-of-function pause. It’s a bad idea fostered by individuals who continue to believe, among other things, that influenza H5N1 virus adapted to transmit by aerosol among ferrets can also infect humans by the same route. Instead of stopping important research, a debate on the merits and risks of gain-of-function experiments should have been conducted while experiments were allowed to proceed.

Towards the end of last year a paper was published a paper on the potential of SARS-virus-like bat coronaviruses to cause human disease. The paper reawakened the debate on the risks and benefits of engineering viruses. Opponents of gain-of-function research began to make incorrect statements about this work. Richard Ebright said that ‘The only impact of this work is the creation, in a lab, of a new, non-natural risk”. Simon Wain-Hobson wrote that a novel virus was created that “grows remarkably well” in human cells; “if the virus escaped, nobody could predict the trajectory”. I have written extensively about why these are other similar statements ignore the value of the work. In my opinion these critics either did not read the paper, or if they did, did not understand it.

Several months later I was asked to write the commentary on a second paper examining the potential of SARS like viruses in bats to cause human disease. I agreed to write it because the science is excellent, the conclusions are important, and it would provide me with another venue for criticizing the gain-of-function pause.

In the PNAS paper, Menachery et al. describe a platform comprising metagenomics data, synthetic virology, transgenic mouse models, and monoclonal antibody therapy to assess the ability of SARS-CoV–like viruses to infect human cells and cause disease in mouse models. The results indicate that a bat SARS-like virus, WIV1-CoV, can infect human cells but is attenuated in mice. Additional changes in the WIV1-CoV genome are likely required to increase the pathogenesis of the virus for mice. The same experimental approaches could be used to examine the potential to infect humans of other animal viruses identified by metagenomics surveys. Unfortunately my commentary is behind a paywall, so for those who cannot read it, I’d like to quote from my final paragraphs on the gain-of-function issue:

The current government pause on these gain-of-function experiments was brought about in part by several vocal critics who feel that the risks of this work outweigh potential benefits. On multiple occasions these individuals have indicated that some of the SARS-CoV work discussed in the Menachery et al. article is of no merit. … These findings provide clear experimental paths for developing monoclonal antibodies and vaccines that could be used should another CoV begin to infect humans. The critics of gain-of-function experiments frequently cite apocalyptic scenarios involving the release of altered viruses and subsequent catastrophic effects on humans. Such statements represent personal opinions that are simply meant to scare the public and push us toward unneeded regulation. Virologists have been manipulating viruses for years—this author was the first to produce, 35 y ago, an infectious DNA clone of an animal virus—and no altered virus has gone on to cause an epidemic in humans. Although there have been recent lapses in high-containment biological facilities, none have resulted in harm, and work has gone on for years in many other facilities without incident. I understand that none of these arguments tell us what will happen in the future, but these are the data that we have to calculate risk, and it appears to be very low. As shown by Menacherry et al. in PNAS, the benefits are considerable.

A major goal of life science research is to improve human health, and prohibiting experiments because they may have some risk is contrary to this goal. Being overly cautious is not without its own risks, as we may not develop the advances needed to not only identify future pandemic viruses and develop methods to prevent and control disease, but to develop a basic understand- ing of pathogenesis that guides prevention. These are just some of the beneficial outcomes that we can predict. There are many examples of how science has progressed in areas that were never anticipated, the so-called serendipity of science. Examples abound, including the discovery of restriction enzymes that helped fuel the biotechnology revolution, and the development of the powerful CRISPR/Cas9 gene-editing technology from its obscure origins as a bacterial defense system.

Banning certain types of potentially risky experiments is short sighted and impedes the potential of science to improve human health. Rather than banning experiments, such as those described by Menachery et al., measures should be put in place to allow their safe conduct. In this way science’s full benefits for society can be realized, unfettered by artificial boundaries.

TWiV 301: Marine viruses and insect defense

On episode #301 of the science show This Week in Virology, Vincent travels to the International Congress of Virology in Montreal and speaks with Carla Saleh and Curtis Suttle about their work on RNA interference and antiviral defense in fruit flies, and viruses in the sea, the greatest biodiversity on Earth.

You can find TWiV #301 at www.microbe.tv/twiv.

An RNA virus that infects Archaea?

Nymph Lake, Yellowstone National ParkEvery different life form on earth can probably be infected with at least one type of virus, if not many more. Most of these viruses have not yet been discovered: just over 2,000 viral species are recognized. While the majority of the known viruses infect bacteria and eukaryotes, there are only about 50 known viruses of the Archaea, and these all have DNA genomes. The first archaeal RNA viruses might have been recently discovered in a hot, acidic spring in Yellowstone National Park.

Archaea are single-cell organisms that are similar in size and shape to bacteria, but are evolutionarily and biochemically quite distinct. They inhabit a broad range of environments including those with extreme conditions such as high temperature, acidity, and salinity. Identification of archaeal RNA viruses is important because their study could provide information about the ancestors of RNA viruses that infect eukaryotes. Direct sequencing of viral communities from the environment, known as viral metagenomics, is one approach being taken to discover archaeal viruses.

The acidic (pH <4) and hot (>80°C) springs in Yellowstone National Park were examined for the presence of archaeal RNA viruses because these bodies of water contain mainly Archaea. Samples were obtained from 28 different sites and extracted nucleic acids were treated with DNAase (to remove DNA genomes) and then reverse transcriptase (to copy RNA to DNA). If reverse transcription was reduced by treatment with RNAse, it was concluded that the sample contained mostly RNA. The results narrowed the sample size to three, all from Nymph Lake. New samples obtained twelve months later also showed a predominance of RNA and were used for metagenomic analysis by deep sequencing.

Analysis of the RNA viral sequences revealed coding regions for a predicted RNA dependent RNA polymerase (RdRp), a hallmark of RNA viruses. One assembled sequence of 5,662 nucleotides, believed to be a complete viral genome, encodes a single open reading frame containing a RdRp and a putative capsid protein similar to that of the positive-strand RNA containing nodaviruses, tetraviruses, and birnaviruses. Another viral sequence encoded a protein with 70% amino acid homology to the predicted RdRp. The sequences are from a novel virus which does not belong to any known virus family.

These results clearly show that at least two related but distinct RNA viruses are present in Nymph Lake. However whether or not the hosts of these viruses are Archaea or Bacteria cannot be determined by these metagenomic analyses. What is needed to resolve this question is old-fashioned virology:  isolating RNA virus particles that can infect an archaeal host and produce new infectious viruses.

B Bolduc, DP Shaughnessy, YI Wolf, EV Koonin, FF Roberto and M Young J. Virol. 2012, 86(10):5562. DOI: 10.1128/JVI.07196-11.

TWiV 195: They did it in the hot tub

On episode #195 of the science show This Week in Virology, the complete TWiV team meets with Ken Stedman to discuss the discovery in Boiling Spring Lake of a DNA virus with the capsid of an RNA virus.

You can find TWiV #195 at www.microbe.tv/twiv.

The abundant and diverse viruses of the seas

earthWhat is the most abundant biological entity in the oceans?

Viruses, of course! The quantity and diversity of viruses in the seas are staggering. Each milliliter of ocean water contains several million virus particles – a global total of 1030 virions! If lined up end to end, they would stretch 200 million light years into space. Viruses constitute 94% of all nucleic-acid containing particles in the sea and are 15 fold more abundant than bacteria and archaea.

Because viruses kill cells, they have a major impact on ocean ecology. About 1023 virus infections occur each second in the oceans; in surface waters they eliminate 20-40% of prokaryotes daily. Viral lysis converts living organisms into particulate matter that becomes carbon dioxide after respiration and photodegradation. Cell killing by viruses also liberates enough iron to supply the needs of phytoplankton, and leads to the production of dimethyl sulphoxide, a gas that influences the climate of the Earth. Because of these activities, marine viruses have a significant impact on global microbial communities and geothermal cycles.

Most of the marine viruses are bacteriophages, but there are also significant numbers that infect eukaryotic phytoplankton, invertebrates, and vertebrates. The best studied viruses are those that infect commercially important species. Novel viruses are frequently discovered; for example, white spot syndrome virus of panaeid shrimp is a member of a new virus family. Viruses of commercially important finfish include herpesviruses, reoviruses, nodaviruses, birnaviruses, and rhabdoviruses. How these viruses are transmitted among marine species is not understood. Many viruses move between marine and fresh waters, posing threats to fishing industries. The rhabdovirus viral hemorrhagic septicemia virus, which causes disease in European farmed trout, has been isolated from 40 marine fish species, from fish farms in Alaska, and from fish in the Great Lakes.

Many ocean viruses cause disease in marine mammals. Phocid distemper virus is a morbillivirus of Arctic phocid seals that has killed thousands of harbor seals in Europe. Similar viruses kill dolphins and other cetaceans. Many other viruses infect marine mammals and even cause disease in humans, including adenoviruses, herpesviruses, parvoviruses, and caliciviruses. The natural reservoirs of most of these viruses are unknown.

Massive sequencing projects have been used to provide information on the diversity of marine viruses. In these studies, seawater is filtered to remove large particles, virions are purified by centrifugation, and nucleic acids are extracted, amplified, and subjected to pyrosequencing. Bioinformatic approaches are used to sift through megabase data sets to identify viral sequences. In one study the viral genomes (‘viromes’) from the Arctic Ocean, the Sargasso Sea, and the coastal waters of British Columbia and the Gulf of Mexico were compared. Over 90% of the sequences were not found in the GenBank collection. There was also little sequence overlap among the samples from the four sites. Similar studies have revealed a rich array of RNA viruses in two different coastal environments; again, most of the sequences were not present in current databases. From the results of these studies it has been estimated that the oceans probably harbor several hundred thousand viral species.

Much more work is required to understand the diversity of marine viruses and their role in the global ecosystem. From the studies done to date, one conclusion is quite clear: the numbers of viruses in the oceans, and their impact on marine life, is far greater than we we ever imagined. And the zoonotic pool may be much larger than we suspected.

Suttle, C. (2007). Marine viruses — major players in the global ecosystem Nature Reviews Microbiology, 5 (10), 801-812 DOI: 10.1038/nrmicro1750

Angly, F., Felts, B., Breitbart, M., Salamon, P., Edwards, R., Carlson, C., Chan, A., Haynes, M., Kelley, S., Liu, H., Mahaffy, J., Mueller, J., Nulton, J., Olson, R., Parsons, R., Rayhawk, S., Suttle, C., & Rohwer, F. (2006). The Marine Viromes of Four Oceanic Regions PLoS Biology, 4 (11) DOI: 10.1371/journal.pbio.0040368

Culley, A., Lang, A.S., & Suttle, C.A. (2006). Metagenomic Analysis of Coastal RNA Virus Communities Science, 312 (5781), 1795-1798 DOI: 10.1126/science.1127404